I think we all understood you well. One transaction, where the minimum is 0.001btc is correct. Everything else is considered a donation to the mixer.
This is very clearly emphasized in the mixing process, so there really shouldn't be any confusion
I believe they should add that part of donations on the mixing page. It only appears in the FAQ section
Don't send the amount less than the allowed minimum. All lesser amount of bitcoins will be considered as donations
For example, in case you have an amount of 0.0009BTC in two different wallets, the best(only) option is to first consolidate and combine them into one wallet and after that send as much as you want to the mixer.
Correct me if I am wrong, if I have UTXOs of 0.0009 BTC in and 0.0005 BTC in an address and then decided to mix them. This should be fine, the output will be more than the minimum with some change if I am to spend exactly 0.001 BTC in the mixer's deposit address. There's no need to first consolidate.